Which integrations are available for this server?

Provides access to biomedical literature through PubMed, enabling search and retrieval of articles, and citation data via the article_search and article_get tools. Integrates with Semantic Scholar for federated literature search and citation analysis, supporting article search and citation graph data.

1. Click on "Install Server". 2. Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state. 3. In the chat, type @ followed by the MCP server name and your instructions, e.g., "@BioMCP get info on BRCA1 gene" That's it! The server will respond to your query, and you can continue using it as needed. Here is a step-by-step guide with screenshots.

BioMCP

by yeyuan98

Overview Schema Related Servers Score Discussions

TypeScript

Remote

BioMCP

A high-performance MCP server that gives LLMs access to 25 biomedical tools federated across 50+ upstream APIs — genes, variants, drugs, diseases, literature, clinical trials, and structural biology in a single integration.

Adapted from the BioMCP Rust with agent-first development approach and enhancements. Kudos to the original authors.

Highlights

25 tools across 8 domains — search, retrieve, and cross-reference biomedical entities
50+ upstream sources — MyGene, MyVariant, MyChem, MyDisease, ClinVar, gnomAD, UniProt, Reactome, OpenTargets, CIViC, OncoKB, DisGeNET, GTEx, STRING, DGIdb, ClinicalTrials.gov, PubMed, EuropePMC, Semantic Scholar, PubTator, LitSense, Monarch Initiative, OpenFDA, NIH Reporter, AlphaGenome, and more
Section-based fetching — entityGet(id, sections) fans out to multiple sources with per-section timeouts and graceful degradation (failed sections return { _error } instead of crashing)
Federated article search — queries 5 literature backends simultaneously with PMID/PMCID/DOI deduplication
Zero-config startup — works out of the box; optional API keys unlock higher rate limits and premium data
350+ unit tests (mocked) + 90+ integration tests (live APIs via in-process MCP client, with automatic retry on 429 rate limits)

Related MCP server: BioBTree

Quick Start

Install and build

git clone <repo-url> && cd biomcp-ts
make install build

Configure with Claude Desktop

Add to your Claude Desktop claude_desktop_config.json:

{
  "mcpServers": {
    "biomcp": {
      "command": "npx",
      "args": ["biomcp"]
    }
  }
}

Or from a local checkout:

{
  "mcpServers": {
    "biomcp": {
      "command": "node",
      "args": ["/path/to/biomcp-ts/dist/bundle.js"]
    }
  }
}

Direct stdio

npm start

Any MCP-compatible client

BioMCP speaks standard MCP over stdio. Point any MCP client at the biomcp binary or node dist/bundle.js.

Available Tools

Gene (7)

Tool	Description
`gene_search`	Search genes by symbol, name, or keyword with type/chromosome filters
`gene_get`	Get detailed gene info by HGNC symbol with optional sections (core, pathways, protein, ontology, GO, interactions, expression, protein_atlas, constraint, druggability, dosage_sensitivity, clinical evidence, disease associations, diseases, funding). Set `smart=true` to auto-resolve gene aliases (e.g., "HER2" → "ERBB2")
`gene_diseases`	Get diseases associated with a gene (DisGeNET / OpenTargets)
`gene_drugs`	Find drugs targeting a gene (OpenTargets)
`gene_trials`	Find clinical trials for a gene
`gene_articles`	Find articles about a gene
`gene_enrich`	Pathway enrichment analysis for a gene list (Reactome)

Variant (4)

Tool	Description
`variant_search`	Search variants by rsid, HGVS, gene, ClinVar significance, frequency, CADD
`variant_get`	Get detailed variant info with optional sections (frequency, predictions, clinical, alphagenome_scores)
`variant_oncokb`	Get OncoKB cancer variant annotations (requires `ONCOKB_TOKEN`)
`variant_trials`	Find clinical trials for a variant

Drug (3)

Tool	Description
`drug_search`	Search drugs by name, mechanism, or keyword
`drug_get`	Get detailed drug info with optional sections (us_regulatory, eu_regulatory, who_regulatory, safety, targets, indications)
`drug_trials`	Find clinical trials for a drug

Disease (4)

Tool	Description
`disease_search`	Search diseases by name, phenotype, or keyword
`disease_get`	Get detailed disease info by ID (DOID, MONDO, OMIM, etc.) with optional sections (gene_associations, phenotypes, pathways, survival)
`disease_drugs`	Get drugs for a disease (OpenTargets)
`disease_trials`	Get clinical trials for a disease (ClinicalTrials.gov)

Article (2)

Tool	Description
`article_search`	Federated literature search across PubMed, EuropePMC, Semantic Scholar, PubTator, and LitSense with optional date range filtering. Accepts `query`, `source`, `limit`, `offset`, and `dateRange` parameters.
`article_get`	Get detailed article info by identifier (PMID, PMCID, or DOI) with optional sections: `oa` (open access / license info), `annotations`, `graph` (citation graph), `citation` (fast-mode or full citation data with `citation_mode` and `citation_direction` options)

Trial (2)

Tool	Description
`trial_search`	Search clinical trials by condition, intervention, status, or phase. Uses cursor-based pagination via `page_token` parameter
`trial_get`	Get detailed trial info by NCT ID with optional sections (eligibility, locations, outcomes)

Utility (2)

Tool	Description
`discover`	Free-text concept resolution across all entity types
`batch_get`	Retrieve multiple entities in parallel

Structural Biology (1)

Tool	Description
`pdb`	Search PDB structures, get entry metadata with optional sections (polymer entities, ligands, assembly, experiment, citation), and download structure files (mmCIF/PDB)

Citation Module

Modes:

Fast (default): Europe PMC, Semantic Scholar, Crossref (~4s)
- Returns: Citations with title, authors, journal, year when available
- Note: Crossref requires DOI; Europe PMC auto-resolves DOI/PMCID to PMID
Full (citation_mode="full"): All 5 providers (~15-30s)
- Adds: PubMed (PMID only) and OpenCitations (DOI only)
- Use for: Comprehensive citation analysis

Provider Data Coverage:

Provider	Forward	Backward	Count	Required ID
Europe PMC	✓	✓	✓	PMID/DOI/PMCID
Semantic Scholar	✓	✓	✓	PMID/DOI/PMCID
Crossref	✓	✓	✓	DOI only
PubMed	✓	✓	✓	PMID only
OpenCitations	✓	✓	✓	DOI only

Automatic Fallback: Fast mode automatically queries PubMed when other providers return counts but no items (requires PMID).

Development

make              # Show available targets
make install      # Install dependencies
make build        # Compile and bundle into dist/bundle.js
make typecheck    # Type-check without emitting
make test         # Run unit tests (fast, mocked)
make test-integration  # Run integration tests (live APIs, ~60s)
make test-all     # Run all tests
make clean        # Remove build artifacts

Local Testing with npx

After building, you can test the MCP server locally via npx:

make build        # Creates dist/bundle.js
npx .             # Runs the bundled MCP server

This is the recommended workflow for local development and testing.

Environment Variables

All keys are optional. BioMCP works without any keys — they unlock higher rate limits and additional data sources.

Variable	Source	Benefit
`NCBI_API_KEY`	NCBI	Higher PubMed / NCBI rate limits
`S2_API_KEY`	Semantic Scholar API key (prevents 429 rate limits)
`OPENFDA_API_KEY`	OpenFDA	OpenFDA API access
`NCI_API_KEY`	NCI CTS	NCI Clinical Trials API
`ONCOKB_TOKEN`	OncoKB	OncoKB cancer variant annotations
`DISGENET_API_KEY`	DisGeNET	Disease-gene associations
`UMLS_API_KEY`	UMLS	UMLS terminology services
`ALPHAGENOME_API_KEY`	AlphaGenome	AlphaGenome variant scores

License

MIT

Install Server

license - permissive license

quality

maintenance

How are these scores calculated?

Maintenance

–Maintainers

–Response time

–Release cycle

–Releases (12mo)

Commit activity

Resources

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